Abstract

Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.

Timescale of the intestinal microbiota evolution: from foraging to Western lifestyle, crossing the Neolithic revolution. The trajectory of the gut microbiome structure of modern populations with different lifestyles mimics the evolution of the relationship between microbes and the human host. Each network plot is a Wiggum plot, published in , which indicates patterns of variation of six identified co-abundance groups (CAGs) in the Hadza (orange; ), Malawi (red; ), Burkina Faso (brown; ), Italians (blue; ), US people (green; ), and Italian children (cyan; ). CAGs are named by the name of the most abundant genera and are color coded as follows: Faecalibacterium (cyan), Dialister (green), Prevotella (orange), Clostridiales_unclassified (yellow), Ruminococcaceae_unclassified (pink), and Blautia (violet). Each node represents a bacterial genus and its dimension is proportional to the mean relative abundance within the population. Connections between nodes represent positive and significant Kendall correlations between genera (false discovery rate <0.05). The central path indicates transition from hunter-gatherer (orange) to Western microbiome (blue), crossing the rural African configuration (red).